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Table 1 Pharmacological interactions and consensus interaction ratio on estrogen receptor α and thymidine kinase

From: iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis

Protein Predicted pharmacological interactions Consensus interaction ratio a Related works
ERA R394-Hb (0.80c) 1.0 Form hydrogen bonding networks for ligand binding [26, 27]
  E353-H (0.64) 0.8  
  H524-H (1.00) 1.0  
  L387-V (1.00) 0.9 Form non-polar contacts with A-ring of sterols scaffolds [28, 29].
  L387-H (0.52) 0.2  
  F404-V (0.90) 1.0  
  V346-V (0.98) 0.5  
  L391-V (0.61) 0.9  
  L384-V (0.57) 0.9  
  L525-H (0.53) 0.9  
TK R222-H (1.00) 0.8 Transfer phosphate in the substrate phosphorylation [30, 31, 36]
  R222-E (1.00) 0.0  
  R222-V (0.62) 0.4  
  R163-H (0.99) 0.6  
  R163-E (0.40) 0.0  
  R163-V (0.56) 0.8  
  E83-V (0.54) 0.2  
  Y101-H (0.40) 0.2 Form hydrogen bonds with thymidine; activity was decreased over 90% if Q125 mutated [32]
  Y101-V (0.45) 0.0  
  Q125-H (0.40) 1.0  
  Y172-V (1.00) 1.0 Sandwich the thymine moiety of substrates [33]
  M128-V (0.58) 1.0  
  W88-V (0.87) 0.9 Constitute a pocket for ligand binding [33]
  H58-V (0.68) 0.9  
  1. a The consensus interaction ratio of the residue i is defined as A j /A, where A j is the number of active compounds interacting to the residue i and A is total number of active compounds.
  2. b H, E and V are the interaction types.
  3. c The pharmacological preferences (i.e. W j defined in Equation (1)).